Development of Theoretical Methods for Studying Biological Macromolecules

新的理论技术正在被开发和表征。这些工作通常与软件开发结合在一起，并涉及对新想法的系统测试和评估。这一发展是由当前的需求和利益驱动的。具体项目包括：-开发研究复杂体系中的反应机理的方法。-复杂构象转变的无偏强制采样和沿反应路径的平均作用力的估计-使用模拟退火法确定复杂体系中的反应路径的复制/路径方法的发展-组合量子力学/分子建模(QM/MM)势的发展(高斯离域MM电荷，双链原子法)-用于QM/MM应用的GAMES-UK和CHARMM集成-使用双链原子界面的密度泛函QM/MM-QM/MM界面的替代处理的评估-使用自由能微扰和PME修正计算酸基的PK。-关于硫化物电离势的密度泛函计算-其他方法的开发-开发RMS最佳匹配约束；精确力，相对约束-合理的药物设计：CHARMM的形状描述符工具的开发-大分子的精确相互作用能计算的发展-小分子/蛋白质结合能预测方法的评估-为两个大分子对接的快速搜索策略的开发-使用GB/SA(广义玻恩/表面积)技术来计算大分子的准确相互作用能已经开发出并应用于计算蛋白质/DNA复合体在水中的溶液中的结合能以及肽-肽二聚能。人们一直在努力改进用量子力学(QM)和经典力学(MM)混合建模复杂系统的技术。QM/MM方法提供了用量子力学方法处理生物系统中感兴趣区域的可能性，从而允许准确地表示键断裂、形成和电子转移，同时还包括来自周围经典区域的重要结构和电荷效应。GamesS-UK已紧密集成到CHARMM中，以便研究小分子和酶复合体中的催化路径。这扩展了CHARMM中的QM/MM套件，因为GamesS-UK提供了DFT(密度泛函理论)。对经典部分电荷的高斯卷积(模糊)进行了实现和测试。这些离域电荷减少了伪影，改进了处理QM/MM边界条件的双链原子方法。该界面已经在一系列小分子上进行了测试，这些小分子由一系列烷烃、醇、胺和氨基酸组成，每个小分子都有不同的QM方法，涉及不同的复杂程度。结果表明，我们将分子划分为量子力学和分子力学区域的方法和实现是稳健的，将对研究酶的机制非常有帮助。一种A类β-内酰胺酶正被用作检查反应路径的测试案例。我们还用从头算和密度泛函方法研究了一系列硫化物和二硫化物的垂直电离势。与现有实验数据的比较表明，B3LYP/6-311G(d，p)水平与其他理论水平相比具有很好的一致性。我们建议用B3LYP/6-311G(d，p)方法预测难以获得实验数据的硫化物的垂直电离势。

New theoretical techniques are being developed and characterized. These efforts are usually coupled with software development, and involve the systematic testing and evaluation of new ideas. This development is driven by current needs and interests. Specific projects include: - Development of methods for examining reaction mechanism in complex systems. - Unbiased forced sampling of complex conformational transitions and estimation of the potential of mean force along the reaction pathway - Development of the REPLICA/PATH method for determining reaction paths in complex systems using simulated annealing - Development of combined Quantum Mechanical/Molecular Modeling (QM/MM) potentials (Gaussian delocalize MM charges, double link atom method) - GAMESS-UK and CHARMM integration for QM/MM applications - Density functional QM/MM using a double link atom interface - Evaluation of alternate treatments of QM/MM interfaces - Calculation of pK of acids groups using Free Energy Perturbation and PME corrections. - Density functional calculations on the ionization potential of sulfides- Other method development - Development of RMS best-fit restraints; accurate forces, relative restraints - Rational drug design: shape descriptor facility for CHARMM - Development of accurate interaction energy calculations for macromolecules - Evaluation of small molecule/protein binding energy prediction methods - Development of a rapid search strategy for docking two macromolecules Accurate interaction energy calculations for macromolecules using GB/SA (Generalized Born/Surface Area) techniques have been developed and applied to calculating binding energies in solution between protein/DNA complex in water and for peptide-peptide dimerization energies. There has been a continuation of effort towards improving the techniques used to model complex systems with a mixture of quantum mechanics (QM) and classical mechanics (MM). QM/MM methods offer the possibility of treating a region of interest within a biological system quantum mechanically thereby allowing the accurate representation of bond breaking, formation, and electron transfer while also including important structural and charge effects from a surrounding classical region. GAMESS-UK has been tightly integrated into CHARMM to allow studies of catalytic paths in small molecules and enzyme complexes. This extends the QM/MM suite within CHARMM since GAMESS-UK provides DFT (Density Functional Theory). Gaussian convolution (blurring) of classical partial charges has been implemented and tested. These delocalized charges reduce artifacts and improve on the double link atom methodology for treating QM/MM boundary conditions. The interface has been tested on a set of small molecules consisting of a series of alkanes, alcohols, amines, and amino acids, each with a variety of QM methods involving different levels of sophistication. The results indicate that our method and implementation of partioning a molecule into quantum and molecular mechanics regions is robust and would be extremely helpful in studying enzyme mechanisms. A Class A beta-lactamase is being used as a test case for examination of reaction paths. We have also examined the vertical ionization potential of a series of sulfides and disulfides using ab initio and density functional methods. Comparison with available experimental data suggests that B3LYP/6-311+G(d,p) level produces excellent agreement compared to other levels of theory. We propose B3LYP/6-311+G(d,p) should be the level of choice in predicting vertical ionization potential of sulfides for which experimental data is hard to come by.